Rosetta 3.4
Public Member Functions | Protected Types | Protected Member Functions | Protected Attributes
protocols::medal::MedalMover Class Reference

#include <MedalMover.hh>

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List of all members.

Public Member Functions

 MedalMover ()
void apply (core::pose::Pose &pose)
std::string get_name () const
 Each derived class must specify its name. The class name.
protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected.
protocols::moves::MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function _should_ be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

Protected Types

typedef utility::vector1< double > Probabilities

Protected Member Functions

void do_loop_closure (core::pose::Pose *pose) const
 Closes chainbreaks in <pose>
void compute_per_residue_probabilities (const unsigned num_residues, const core::sequence::SequenceAlignment &alignment, const protocols::loops::Loops &chunks, const core::kinematics::FoldTree &tree, const core::fragment::FragSet &fragments, Probabilities *probs) const
 Computes per-residue sampling probabilities.
void decompose_structure (const core::pose::Pose &pose, protocols::loops::LoopsOP &chunks) const
 Partitions the structure into non-overlapping chunks.
protocols::moves::MoverOP create_fragment_mover (core::pose::PoseOP native, core::scoring::ScoreFunctionOP score, core::fragment::FragSetOP fragments, const Probabilities &probs, const std::string &policy, unsigned library_size) const
 Configures a mover for biased fragment insertion.
protocols::moves::MoverOP create_fragment_and_rigid_mover (const core::pose::Pose &pose, core::pose::PoseOP native, core::scoring::ScoreFunctionOP score, core::fragment::FragSetOP fragments, const Probabilities &probs, const std::string &policy, unsigned library_size) const
 Configures a mover for alternating biased fragment insertion and rigid body moves.
protocols::moves::MoverOP create_small_mover (core::pose::PoseOP native, core::scoring::ScoreFunctionOP score) const
 Configures a mover for performing alternating small and shear moves.
core::scoring::ScoreFunctionOP score_function () const
 Configures a basic score functions which callers can then specialize.

Protected Attributes

core::fragment::FragSetOP fragments_sm_
core::fragment::FragSetOP fragments_lg_

Member Typedef Documentation


Constructor & Destructor Documentation

protocols::medal::MedalMover::MedalMover ( )

References fragments_lg_, and fragments_sm_.

Referenced by clone(), and fresh_instance().


Member Function Documentation

void protocols::medal::MedalMover::apply ( core::pose::Pose pose) [virtual]
protocols::moves::MoverOP protocols::medal::MedalMover::clone ( ) const [virtual]

clone has to be overridden only if clone invocation is expected.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

References MedalMover().

void protocols::medal::MedalMover::compute_per_residue_probabilities ( const unsigned  num_residues,
const core::sequence::SequenceAlignment alignment,
const protocols::loops::Loops chunks,
const core::kinematics::FoldTree tree,
const core::fragment::FragSet fragments,
Probabilities probs 
) const [protected]
protocols::moves::MoverOP protocols::medal::MedalMover::create_fragment_and_rigid_mover ( const core::pose::Pose pose,
core::pose::PoseOP  native,
core::scoring::ScoreFunctionOP  score,
core::fragment::FragSetOP  fragments,
const Probabilities probs,
const std::string &  policy,
unsigned  library_size 
) const [protected]

Configures a mover for alternating biased fragment insertion and rigid body moves.

References core::pose::Pose::fold_tree(), and protocols::medal::on_pose_accept().

Referenced by apply().

protocols::moves::MoverOP protocols::medal::MedalMover::create_fragment_mover ( core::pose::PoseOP  native,
core::scoring::ScoreFunctionOP  score,
core::fragment::FragSetOP  fragments,
const Probabilities probs,
const std::string &  policy,
unsigned  library_size 
) const [protected]

Configures a mover for biased fragment insertion.

References protocols::medal::on_pose_accept().

protocols::moves::MoverOP protocols::medal::MedalMover::create_small_mover ( core::pose::PoseOP  native,
core::scoring::ScoreFunctionOP  score 
) const [protected]

Configures a mover for performing alternating small and shear moves.

References protocols::medal::on_pose_accept().

Referenced by apply().

void protocols::medal::MedalMover::decompose_structure ( const core::pose::Pose pose,
protocols::loops::LoopsOP chunks 
) const [protected]

Partitions the structure into non-overlapping chunks.

References protocols::nonlocal::chunks_by_CA_CA_distance().

Referenced by apply().

void protocols::medal::MedalMover::do_loop_closure ( core::pose::Pose pose) const [protected]
protocols::moves::MoverOP protocols::medal::MedalMover::fresh_instance ( ) const [virtual]

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function _should_ be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

References MedalMover().

std::string protocols::medal::MedalMover::get_name ( ) const [virtual]

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

core::scoring::ScoreFunctionOP protocols::medal::MedalMover::score_function ( ) const [protected]

Configures a basic score functions which callers can then specialize.

Configures the score function used during the simulation. Precedence: 1. User-specified patch file (i.e. -rigid:patch) 2. User-specified options (e.g. -jumps:increase_chainbreak) 3. Default values

References core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(), core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep(), core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, and core::scoring::linear_chainbreak.

Referenced by apply().


Member Data Documentation

Referenced by MedalMover().

Referenced by apply(), do_loop_closure(), and MedalMover().


The documentation for this class was generated from the following files:
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